Imputation Report For Cohort: ORPS_cohort

Per chromosome imputation report for cohort ORPS_cohort.

Chromosome index, 23 in total. Skip to the section for a particular chromosome using the buttons below.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X

Cohort Metadata

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Information captured during the processing of this cohort.

Property Value
FORMAT MINIMAC2

UPLOADED 8.4.2021

Genome-Wide

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A: Alternate Allele Frequency: Genome-Wide

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 7206718 61.046
0.1 1217131 10.310
0.2 808714 6.850
0.3 618842 5.242
0.4 496324 4.204
0.5 408209 3.458
0.6 347234 2.941
0.7 293099 2.483
0.8 246053 2.084
0.9 163030 1.381
Total 11805354 100.000

B: Imputation INFO Score: Genome-Wide

Variants binned by imputation INFO score

INFO Score Count %
0.3 320086 2.711
0.4 341848 2.896
0.5 430733 3.649
0.6 657402 5.569
0.7 1041614 8.823
0.8 1756496 14.879
0.9 7228707 61.232
1.0 28468 0.241
Total 11805354 100.000

Chromosome 1

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 547837 61.5314
0.1 89884 10.0955
0.2 57403 6.4473
0.3 45919 5.1575
0.4 37602 4.2233
0.5 30404 3.4149
0.6 27326 3.0692
0.7 21846 2.4537
0.8 18653 2.0950
0.9 13463 1.5121
Total 890337

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 25264 2.8376
0.4 26183 2.9408
0.5 33281 3.7380
0.6 50587 5.6818
0.7 80200 9.0078
0.8 134554 15.1127
0.9 538310 60.4614
1.0 1958 0.2199
Total 890337

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 2

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 599164 61.5986
0.1 101638 10.4492
0.2 64623 6.6437
0.3 50351 5.1765
0.4 38241 3.9315
0.5 32123 3.3025
0.6 29074 2.9890
0.7 22786 2.3426
0.8 21149 2.1743
0.9 13542 1.3922
Total 972691

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 25533 2.6250
0.4 27552 2.8326
0.5 33386 3.4323
0.6 50931 5.2361
0.7 82426 8.4740
0.8 141643 14.5620
0.9 608970 62.6067
1.0 2250 0.2313
Total 972691

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 3

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 503683 60.9231
0.1 87368 10.5676
0.2 56248 6.8035
0.3 42531 5.1443
0.4 34736 4.2015
0.5 29219 3.5342
0.6 24751 2.9938
0.7 20377 2.4647
0.8 16735 2.0242
0.9 11104 1.3431
Total 826752

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 21545 2.6060
0.4 22678 2.7430
0.5 28252 3.4172
0.6 43574 5.2705
0.7 70686 8.5498
0.8 119655 14.4729
0.9 518045 62.6603
1.0 2317 0.2803
Total 826752

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 4

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 500119 60.3195
0.1 81325 9.8086
0.2 60187 7.2592
0.3 45753 5.5183
0.4 33594 4.0518
0.5 27603 3.3292
0.6 24996 3.0148
0.7 21926 2.6445
0.8 19959 2.4073
0.9 13655 1.6469
Total 829117

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 20648 2.4904
0.4 22170 2.6739
0.5 27962 3.3725
0.6 42240 5.0946
0.7 69175 8.3432
0.8 119958 14.4682
0.9 525348 63.3623
1.0 1616 0.1949
Total 829117

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 5

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 466432 61.6097
0.1 76338 10.0833
0.2 52147 6.8880
0.3 40114 5.2986
0.4 31572 4.1703
0.5 24954 3.2961
0.6 22188 2.9308
0.7 18511 2.4451
0.8 15347 2.0271
0.9 9472 1.2511
Total 757075

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 19404 2.5630
0.4 20460 2.7025
0.5 25511 3.3697
0.6 39307 5.1920
0.7 63248 8.3543
0.8 108111 14.2801
0.9 478855 63.2507
1.0 2179 0.2878
Total 757075

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 6

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 455065 60.5524
0.1 79069 10.5212
0.2 52713 7.0142
0.3 40752 5.4226
0.4 32715 4.3532
0.5 26387 3.5111
0.6 21900 2.9141
0.7 17771 2.3647
0.8 15079 2.0065
0.9 10072 1.3402
Total 751523

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 17815 2.3705
0.4 18604 2.4755
0.5 22926 3.0506
0.6 35135 4.6752
0.7 56156 7.4723
0.8 96860 12.8885
0.9 499269 66.4343
1.0 4758 0.6331
Total 751523

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 7

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 403103 60.6250
0.1 68447 10.2941
0.2 48425 7.2829
0.3 35172 5.2897
0.4 29620 4.4547
0.5 23629 3.5537
0.6 18868 2.8377
0.7 15855 2.3845
0.8 12604 1.8956
0.9 9189 1.3820
Total 664912

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 17748 2.6692
0.4 18555 2.7906
0.5 23518 3.5370
0.6 36492 5.4882
0.7 58533 8.8031
0.8 98326 14.7878
0.9 410592 61.7513
1.0 1148 0.1727
Total 664912

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 8

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 395977 61.5020
0.1 64862 10.0742
0.2 44858 6.9672
0.3 31946 4.9618
0.4 27650 4.2945
0.5 22651 3.5181
0.6 18438 2.8637
0.7 15888 2.4677
0.8 13286 2.0635
0.9 8288 1.2873
Total 643844

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 16825 2.6132
0.4 18293 2.8412
0.5 22422 3.4825
0.6 33323 5.1756
0.7 54054 8.3955
0.8 91390 14.1944
0.9 405713 63.0142
1.0 1824 0.2833
Total 643844

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 9

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 307821 61.4686
0.1 55162 11.0153
0.2 32490 6.4879
0.3 25233 5.0388
0.4 20476 4.0888
0.5 16168 3.2286
0.6 14540 2.9035
0.7 11846 2.3655
0.8 9808 1.9586
0.9 7234 1.4446
Total 500778

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 13603 2.7164
0.4 14186 2.8328
0.5 17392 3.4730
0.6 27816 5.5546
0.7 45022 8.9904
0.8 75939 15.1642
0.9 306144 61.1337
1.0 676 0.1350
Total 500778

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 10

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 348871 60.6249
0.1 60089 10.4419
0.2 40187 6.9835
0.3 28434 4.9411
0.4 25344 4.4041
0.5 20777 3.6105
0.6 16672 2.8972
0.7 14263 2.4785
0.8 12776 2.2201
0.9 8045 1.3980
Total 575458

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 14206 2.4686
0.4 15288 2.6567
0.5 19002 3.3021
0.6 28722 4.9912
0.7 47390 8.2352
0.8 84387 14.6643
0.9 365335 63.4860
1.0 1128 0.1960
Total 575458

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 11

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 351667 61.0488
0.1 57674 10.0121
0.2 36583 6.3508
0.3 31054 5.3909
0.4 24637 4.2769
0.5 20528 3.5636
0.6 18377 3.1902
0.7 14192 2.4637
0.8 12605 2.1882
0.9 8725 1.5146
Total 576042

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 14253 2.4743
0.4 14474 2.5127
0.5 17910 3.1091
0.6 29248 5.0774
0.7 49485 8.5905
0.8 84042 14.5896
0.9 364855 63.3383
1.0 1775 0.3081
Total 576042

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 12

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 335334 61.1450
0.1 55734 10.1626
0.2 35697 6.5090
0.3 29802 5.4341
0.4 24022 4.3802
0.5 18940 3.4535
0.6 15692 2.8613
0.7 12677 2.3115
0.8 12796 2.3332
0.9 7730 1.4095
Total 548424

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 14334 2.6137
0.4 15346 2.7982
0.5 19310 3.5210
0.6 29235 5.3307
0.7 47689 8.6956
0.8 81509 14.8624
0.9 339832 61.9652
1.0 1169 0.2132
Total 548424

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 13

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 252962 60.0539
0.1 42960 10.1988
0.2 28139 6.6803
0.3 22842 5.4228
0.4 17215 4.0869
0.5 15863 3.7659
0.6 12685 3.0115
0.7 11369 2.6990
0.8 9621 2.2841
0.9 7569 1.7969
Total 421225

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 10673 2.5338
0.4 11299 2.6824
0.5 13981 3.3191
0.6 21928 5.2058
0.7 36318 8.6220
0.8 60109 14.2700
0.9 265833 63.1095
1.0 1084 0.2573
Total 421225

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 14

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 225367 61.1672
0.1 39217 10.6440
0.2 25743 6.9870
0.3 18164 4.9299
0.4 15309 4.1550
0.5 11638 3.1587
0.6 9989 2.7111
0.7 9574 2.5985
0.8 7715 2.0939
0.9 5728 1.5546
Total 368444

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 9649 2.6189
0.4 10028 2.7217
0.5 12792 3.4719
0.6 19932 5.4098
0.7 31321 8.5009
0.8 53774 14.5949
0.9 230275 62.4993
1.0 673 0.1827
Total 368444

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 15

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 200536 61.3267
0.1 32287 9.8738
0.2 22715 6.9466
0.3 17283 5.2854
0.4 13679 4.1832
0.5 11868 3.6294
0.6 8876 2.7144
0.7 7832 2.3951
0.8 6801 2.0798
0.9 5119 1.5655
Total 326996

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 9748 2.9811
0.4 10930 3.3425
0.5 13990 4.2783
0.6 20558 6.2869
0.7 30945 9.4634
0.8 51359 15.7063
0.9 188979 57.7925
1.0 487 0.1489
Total 326996

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 16

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 219924 61.7102
0.1 37323 10.4728
0.2 22876 6.4190
0.3 18917 5.3081
0.4 14271 4.0044
0.5 12389 3.4763
0.6 10624 2.9811
0.7 9421 2.6435
0.8 6692 1.8778
0.9 3945 1.1070
Total 356382

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 10183 2.8573
0.4 11339 3.1817
0.5 14191 3.9820
0.6 23118 6.4869
0.7 36692 10.2957
0.8 61907 17.3710
0.9 198615 55.7309
1.0 337 0.0946
Total 356382

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 17

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 186900 61.0365
0.1 30484 9.9553
0.2 22900 7.4785
0.3 15798 5.1592
0.4 12995 4.2438
0.5 11413 3.7272
0.6 8981 2.9330
0.7 8024 2.6204
0.8 5784 1.8889
0.9 2931 0.9572
Total 306210

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 10154 3.3160
0.4 11530 3.7654
0.5 15390 5.0260
0.6 22059 7.2039
0.7 33038 10.7893
0.8 51731 16.8940
0.9 161909 52.8752
1.0 399 0.1303
Total 306210

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 18

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 197665 60.4216
0.1 34186 10.4499
0.2 23588 7.2103
0.3 17549 5.3643
0.4 13970 4.2703
0.5 11147 3.4074
0.6 8972 2.7425
0.7 8474 2.5903
0.8 6775 2.0710
0.9 4817 1.4724
Total 327143

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 9570 2.9253
0.4 9761 2.9837
0.5 13373 4.0878
0.6 20192 6.1722
0.7 30612 9.3574
0.8 51902 15.8652
0.9 191291 58.4732
1.0 442 0.1351
Total 327143

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 19

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 152489 60.3838
0.1 29173 11.5522
0.2 19004 7.5254
0.3 13012 5.1526
0.4 9658 3.8245
0.5 8987 3.5587
0.6 6983 2.7652
0.7 5992 2.3728
0.8 4643 1.8386
0.9 2592 1.0264
Total 252533

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 7931 3.1406
0.4 9298 3.6819
0.5 12534 4.9633
0.6 18814 7.4501
0.7 27945 11.0659
0.8 43966 17.4100
0.9 131590 52.1080
1.0 455 0.1802
Total 252533

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 20

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 158876 61.4180
0.1 27377 10.5833
0.2 17763 6.8668
0.3 13661 5.2810
0.4 11044 4.2694
0.5 8826 3.4119
0.6 7642 2.9542
0.7 5930 2.2924
0.8 4665 1.8034
0.9 2896 1.1195
Total 258680

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 7357 2.8441
0.4 7701 2.9770
0.5 10542 4.0753
0.6 16387 6.3349
0.7 25260 9.7650
0.8 41643 16.0983
0.9 149500 57.7934
1.0 290 0.1121
Total 258680

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 21

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 90188 58.7379
0.1 15932 10.3762
0.2 10516 6.8489
0.3 8531 5.5561
0.4 7459 4.8579
0.5 5994 3.9038
0.6 4940 3.2173
0.7 4635 3.0187
0.8 3885 2.5302
0.9 1463 0.9528
Total 153543

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 4467 2.9093
0.4 4603 2.9979
0.5 6457 4.2053
0.6 9976 6.4972
0.7 14883 9.6931
0.8 24889 16.2098
0.9 88082 57.3663
1.0 186 0.1211
Total 153543

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 22

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 91661 60.7686
0.1 15806 10.4789
0.2 10904 7.2290
0.3 8186 5.4271
0.4 6624 4.3915
0.5 5318 3.5257
0.6 4527 3.0013
0.7 3881 2.5730
0.8 2618 1.7357
0.9 1311 0.8692
Total 150836

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 5029 3.3341
0.4 5451 3.6139
0.5 6853 4.5433
0.6 11016 7.3033
0.7 15837 10.4995
0.8 25721 17.0523
0.9 80781 53.5555
1.0 148 0.0981
Total 150836

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome X

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 215077 62.0876
0.1 34796 10.0448
0.2 23005 6.6410
0.3 17838 5.1494
0.4 13891 4.0100
0.5 11383 3.2860
0.6 10193 2.9425
0.7 10029 2.8951
0.8 6057 1.7485
0.9 4140 1.1951
Total 346409

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 14147 4.0839
0.4 16119 4.6532
0.5 19758 5.7037
0.6 26812 7.7400
0.7 34699 10.0168
0.8 53121 15.3348
0.9 180584 52.1303
1.0 1169 0.3375
Total 346409

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering